Continuity mistake: At the beginning of the third episode, the countdown reads 49:18:32 in the close up, but when the Brigadier walks across the room it now is on 49:15:01. (In other words three minutes thirty one seconds have elapsed). Yet these two events are about ten seconds apart. Also, the timer should never read either of these times. The professor moved the countdown forward to exactly 49 hours (49:00:00).
Continuity mistake: Throughout the serial, Bessie's tires are dry in studio shots (inside the Doctor's shed) and wet on location shots.
Continuity mistake: Liz's hairstyle is different in indoor and outdoor shots.
Revealing mistake: When Stahlman is killed - the second time - the shot of his green primord face reveals the actor's unpainted neck under his beard.
Character mistake: When the Brigade Leader shoots the Primord, he noticeably closes his eye. He is supposed to be a high ranking well trained officer.
Answer: It was never destroyed on-screen; it was intact at the end of the TV movie, and destroyed by the start of the 2005 series. It was destroyed in the novel "The Ancestor Cell," but in a completely different manner to what happened in the series.
DaveJB